Contacts of the helix formed by residues 569 - 581 (chain A) in PDB entry 1R49
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 569 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A GLU* 6.5 1.8 - - + -
505A CYS* 4.1 11.7 - - - -
567A ARG 5.7 0.4 - - - -
568A LEU* 1.3 82.5 + - - +
570A THR* 1.3 68.6 + - - +
571A GLY* 3.1 5.7 - - - +
572A ILE* 3.1 36.7 + - - +
573A LEU* 2.9 22.7 + - - +
2B A 5.7 4.6 + - - +
3B A 5.6 3.2 + - - -
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Residues in contact with THR 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A ALA* 3.7 17.5 - - + -
490A GLY 3.5 26.5 - - - +
491A ASN* 3.3 36.4 + - - +
492A GLU 5.2 0.7 + - - -
505A CYS* 3.7 15.2 - - - +
569A ASN* 1.3 73.9 - - - +
571A GLY* 1.3 56.3 + - - +
573A LEU* 4.2 3.1 - - - -
574A ASN* 2.7 52.8 + - - +
117C C 6.5 0.7 - - - -
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Residues in contact with GLY 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A ASN* 3.1 7.4 + - - +
570A THR* 1.3 82.3 + - - +
572A ILE* 1.3 59.0 + - - +
574A ASN* 4.1 3.8 - - - +
575A LYS* 3.1 23.2 + - - +
118C T 5.9 7.4 - - - -
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Residues in contact with ILE 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A LYS* 4.6 25.4 - - + +
475A ARG* 5.4 8.1 - - - +
567A ARG 5.4 3.1 - - - +
568A LEU* 3.7 20.2 - - + -
569A ASN* 3.1 24.2 + - - +
571A GLY* 1.3 71.6 - - - +
573A LEU* 1.3 70.1 + - - +
575A LYS* 3.0 11.2 + - + +
576A HIS* 2.9 26.7 + - + +
2B A 5.4 7.6 - - - +
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Residues in contact with LEU 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A ARG* 4.4 22.0 - - + +
478A ALA* 5.1 4.0 - - + -
479A LEU* 4.4 31.2 - - + +
482A ILE* 4.7 13.0 - - + -
489A ALA* 5.2 3.4 - - + -
505A CYS* 3.6 25.6 - - - -
568A LEU* 4.6 8.3 - - + -
569A ASN 2.9 17.1 + - - +
570A THR* 3.7 4.0 - - - +
572A ILE* 1.3 80.0 - - - +
574A ASN* 1.3 64.9 + - - +
576A HIS* 3.4 8.6 + - - +
577A LEU* 3.2 32.4 + - + +
586A ALA* 4.4 21.3 - - + -
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Residues in contact with ASN 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ALA* 5.3 0.2 - - - +
570A THR* 2.7 41.8 + - - +
571A GLY* 4.2 3.0 - - - +
573A LEU* 1.3 72.1 - - - +
575A LYS* 1.3 61.3 + - - +
577A LEU* 2.9 21.5 + - - +
578A GLN* 2.9 27.9 + - - +
584A LEU 3.9 0.2 - - - +
585A THR* 4.5 8.3 - - + -
586A ALA* 3.2 32.6 + - - +
117C C 3.3 35.2 + - + +
118C T 5.0 7.8 - - + +
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Residues in contact with LYS 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A GLY 3.1 16.3 + - - +
572A ILE* 3.0 14.7 + - + +
574A ASN* 1.3 76.0 - - - +
576A HIS* 1.3 65.8 + - - +
577A LEU 3.2 0.5 + - - -
578A GLN* 3.6 14.2 + - - +
579A ASP* 3.3 30.7 + - - +
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Residues in contact with HIS 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A GLN* 4.4 4.0 + - - -
461A TYR* 5.8 3.1 - - + -
464A ASP* 4.1 7.6 + - - -
475A ARG* 3.0 63.3 + - + +
479A LEU* 4.6 10.8 - - + +
572A ILE* 2.9 13.4 + - + +
573A LEU* 3.5 9.8 + - - +
574A ASN 3.2 0.2 - - - -
575A LYS* 1.3 80.2 - - + +
577A LEU* 1.3 69.7 + - + +
579A ASP* 3.0 22.1 - - + +
580A LEU* 3.5 37.5 - - + +
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Residues in contact with LEU 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A ILE* 5.8 0.4 - - + -
479A LEU* 4.0 25.6 - - + -
573A LEU* 3.2 20.4 + - + +
574A ASN* 2.9 12.7 + - - +
576A HIS* 1.3 90.6 - - + +
578A GLN* 1.3 57.2 + - - +
579A ASP 2.8 10.3 + - - -
580A LEU* 3.0 18.8 + - + +
581A MET 3.2 11.8 + - - +
584A LEU* 3.2 29.4 - - + +
585A THR 3.6 30.1 - - - +
586A ALA* 3.9 7.2 - - + +
589A PHE* 3.8 21.5 - - + -
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Residues in contact with GLN 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A ASN* 2.9 24.4 + - - +
575A LYS* 3.7 12.4 + - - +
577A LEU* 1.3 72.0 - - - +
579A ASP* 1.3 59.4 + - - +
581A MET 3.1 19.2 - - - +
582A GLU* 4.6 6.3 - - - +
583A GLY* 4.2 13.9 - - - +
584A LEU 3.3 19.8 + - - +
585A THR* 3.7 8.0 - - - +
118C T 3.4 34.1 + - - -
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Residues in contact with ASP 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A LYS* 3.3 24.5 + - - +
576A HIS* 3.0 23.3 - - + +
577A LEU 2.8 0.4 - - - -
578A GLN* 1.3 79.9 - - - +
580A LEU* 1.3 70.1 + - + +
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Residues in contact with LEU 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A CYS* 6.1 0.4 - - - -
456A LYS* 3.7 29.9 + - - +
457A ILE* 3.9 36.8 - - + -
460A GLN* 3.3 29.8 - - + +
576A HIS* 3.5 39.0 - - + +
577A LEU* 3.0 10.7 + - + +
579A ASP* 1.3 85.0 - - + +
581A MET* 1.3 58.7 + - + +
584A LEU* 4.9 2.0 - - + -
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Residues in contact with MET 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A THR* 3.4 31.9 - - + +
449A ARG* 3.5 24.9 - - + +
450A LEU* 3.3 36.6 - - + -
453A CYS* 3.8 20.2 - - - -
577A LEU 3.2 4.1 + - - +
578A GLN* 3.1 25.1 - - - -
580A LEU* 1.3 79.8 - - + +
582A GLU* 1.3 84.2 + - - +
584A LEU* 3.5 28.1 + - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il